rs6525480

Positions:

• chrX-71204561-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (4103 hom., 8706 hem., cov: 20)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71204561G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 31415 AN: 107170 Hom.: 4098 Cov.: 20 AF XY: 0.292 AC XY: 8688 AN XY: 29720

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.292

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.293 AC: 31442 AN: 107224 Hom.: 4103 Cov.: 20 AF XY: 0.292 AC XY: 8706 AN XY: 29782

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.300

Alfa AF: 0.254 Hom.: 1579

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6525480; hg19: chrX-70424411;